There are a few approaches to this. I’ve used a combination of these for my game.

Put all of the models in the same qubicle file and export them together so your texture.png has everything in it.

Open the model in a program like Blender and adjust the UVs so it matches.

I have a set of characters I built in qubicle. I exported them with no mesh optimization so all of the colors in the texture.png are just dots. I later rigged them and brought them into unity. This way I can switch out all of the different armors and clothings for my characters and if I want I just adjust the one color in the texture via code. (I had to map out what color comes from where which was a bit of a pain)

Later I built a series of hats and accessories. Instead of starting from scratch with a brand new FBX that has everything I took them and exported as a FBX, added a few extra colors to the main png manually and then changed the UVs in blender which was a matter of just dragging the squares to the right colors. It took a little bit of learning but knowing blender is great for game development anyways.